186 Works

W7984_WGS_assembly_Genotypes_for_kmer-based_markers

Martin Mascher
Genotypes for 1,716,090 50+1-mer markers across 88 individuals defined as described in the main text (Ultradense Genetic Linkage Map) and in Supplementary Note. Genotypes are encoded as 1 (Synthetic W7984), -1 (Opata M85), or 0 (missing data). Markers are labeled by their defining 50-mer sequence tag.

Screening of wild potato genetic resources for resistance to the white potato cyst nematode

Silvia Bachmann-Pfabe
This data set contains the results of the Globodera pallida (Stone) Behrens resistance screening of wild potato accessions (Solanum spp.) during the years 2000 to 2016 maintained at the Gross Luesewitz Potato Collections (GLKS) of the IPK.

Image analysis results from quantitative monitoring of 484 Arabidopsis thaliana plants using high-throughput plant phenotyping

Astrid Junker
This dataset contains image analysis results based on 30426 raw image files from a high-throughput plant phenotyping experiment. Here, the growth and development of 484 Arabidopsis thaliana plants (C24 genotype) in respect to plant movement and soil cover has been monitored over 55 days. This dataset contains 29724 feature-annotated result images. The features are plant height and volume.

“Blaster” – graphical sequence data workbench

Stefanie Lueck
“Blaster” is a Microsoft Windows-based sequence processing and analysis tool that provides simple and intuitive graphical user interface to some of the most common tools for nucleotide and protein sequence analysis. It includes Local BLAST tool, BOWTIE sequence aligner, Sequence extraction from multiple FASTA files, Reverse and reverse complement sequence convertor, Sequence format conversions (FASTA, CSV), Custom sequence databases.

LAILAPS and e!DAL_ Explore Genome Annotations and Publish Research Data

Daniel Arend & Jinbo Chen
Poster for PAG 2015, San Diego, January 10-14 2015

Genotyping-by-sequencing SNP matrix of 243 diverse barley accessions

Martin Mascher
Genotyping-by-sequnencing (GBS) libraries were constructed for 243 barley accession. Raw reads were trimmed with with cutadapt and mapped to the draft genome assembly of barley cultivar ‘Morex’ with BWA-MEM using default parameters. SNPs were called with SAMtools 0.1.19 and filtered with an AWK script. The minimum read depth for a successful genotype calls was 10. SNPs with more than 5 % missing genotype calls were discarded. The resultant genotype matrix is accessible here as an...

High-throughput phenotyping reveals strong temporal dynamics of QTL action on plant growth in canola

Dominic Knoch
A major challenge of plant biology is to unravel the genetic basis of complex traits. We took advantage of recent technical advances in high-throughput phenotyping in conjunction with genome-wide association studies to elucidate genotype-phenotype relationships at high temporal resolution. A diverse Brassica napus population from a commercial breeding programme was analysed by automated non-invasive phenotyping. Time-resolved data for early growth-related traits, including estimated biovolume, projected leaf area, early plant height, colour uniformity were established and...

Six-rowed domestication allele vrs1 positively regulates leaf width and vein number in barley

Markus Kuhlmann
Crop improvement is one of the recommendations are given to meet the needs of the growing population. Exploring genes that regulate yield related phenotypes is the preceding step to accomplish this goal. By applying a Genome Wide Association Study, we identified a gene encoding the homeobox transcription factor Six-rowed spike 1 (VRS1) that regulates leaf blade area (LA) in two- and six-rowed spring barley (Hordeum vulgare L.). VRS1 has been known as a key domestication...

Genotyping-by-sequencing data of two double introgression-line mapping populations developped to map the Hordeum bulbosum A42 powdery mildew locus

Parastoo Hoseinzadeh, Axel Himmelbach, Hélène Pidon & Nils Stein
This dataset contains the raw GBS data from the mapping populations dIL_4176 and dIL_5216, developped to map the locus of resistance to powdery mildew from the Hordeum bulbosum A42 accession. dIL_4176 is derived from the cross between the introgression line (IL) 200A3/7/M1 (named "IL 88" in the dataset) from the H. bulbosum donor A17 and the resistant IL "4176/26_33", a BC1F6 from the cross between the barley cultivar Borwina and the H. bulbosum accession A42....

Raw images files from quantitative monitoring of 484 Arabidopsis thaliana plants using high-throughput plant phenotyping

Astrid Junker
This dataset contains 30426 raw image files from a high-throughput plant phenotyping experiment. The growth and development of 484 Arabidopsis thaliana plants (C24 genotype) in respect to plant movement and soil cover has been monitored over 55 days. The files are described using the ISA-Tab format and fulfill the MIAPPE recommendations.

The e!DAL JAVA API: Sharing & Citing Research Data in Life Sciences

Daniel Arend
e!DAL Poster for the DILS Conference 2014 in Lisbon, Portugal

15k SNP chip data for spring and winter wheat

Quddoos H. Muqaddasi
In total, 207 wheat genotypes (111 spring and 96 winter type) were analysed using a 15k Infinium SNP array, which is an optimized and reduced version of the 90k iSELECT SNP-chip described by Wang et al. (2014) Plant Biotechnol J 12:787-796. The development of the 15k SNP-chip and genotyping was performed by TraitGenetics GmbH (http://www.traitgenetics.com).

Data Management Experiences and Best Practices from the Perspective of a Plant Research Institute

Daniel Arend
Presentation on the DILS 17.July.2014 in Lisbon, Portugal

Illustrations of 10 important model and crop plant species

Mona Schreiber
The data set contains the illustrations of 10 important model and crop plant species. These plant species were selected for their agronomic and scientific importance. Whole-genome shotgun sequence data of these plants are integrated in the Kmasker plants web server for data analysis. Included are: ‘Arabidopsis thaliana L., Beta vulgaris ssp. vulgaris, Brassica napus L., Glycine max L., Hordeum vulgare L., Oryza sativa L., Secale cereale L., Solanum lycopericum L., Triticum aestivum L. and Zea...

A case study for efficient management of high throughput primary lab data

Christian Colmsee, Steffen Flemming, Matthias Klapperstück, Matthias Lange & Uwe Scholz
Source code for the LimsLight primary data management system

Raw image files from an investigation of vegetative biomass growth in well-watered and drought stress conditions in a Hordeum vulgare set (2011-09-16 to 2011-11-13)

Kerstin Neumann
This dataset contains 211152 raw image files of a high-throughput plant phenotyping experiment, which was run from 2011-09-16 to 2011-11-13. The vegetative biomass growth of a small set of Hordeum vulgare plants has been monitored. The files are described using the ISA-Tab format and fulfill the MIAPPE recommendations. The raw images were processed by the barley analysis pipelines of the IAP software (version 1.1.2; https://doi.org/10.1104/pp.113.233932). The analysed results were exported in the ‘1137KN_IAP_export.xlsx’ file.

Visualising comparative genomics with Hilbert curves

Thomas Schmutzer, Fabian Bull & Uwe Scholz
Poster - Bioinformatics of Human and Animal Genomics 2011

Linear modeling reveals a predominance of cis- over trans-regulatory effects in wild and domesticated barley

Matthew Haas
Barley, like other crops, has experienced a series of genetic changes that have impacted its architecture and growth habit to suit the needs of humans. Domestication also resulted in a concomitant bottleneck that reduced sequence diversity in genes and regulatory regions. Little is known about regulatory changed resulting from domestication in barley. We used RNA-seq to examine allele-specific expression (ASE) in hybrids between wild and domesticated barley. Our results show that most genes have conserved...

Association mapping of wheat Fusarium head blight resistance-related regions using a candidate-gene approach and their verification in a biparental population

Karolina Maria Słomińska-Durdasiak
This is a candidate gene dataset and the corresponding post-peer-review, pre-copyedit version of an article published in Theoretical and Applied Genetics. The final authenticated version is available online at: https://doi.org/10.1007/s00122-019-03463-5

Tutorial with three data sets providing assistance and guidance of data processing using Kmasker plants

Thomas Schmutzer
Three data sets providing assistance and guidance of data processing using Kmasker plants. Also, we perform a comparison of Kmasker plants functionality with the KAT tool. This DOI holds input and output data of this analysis. Example_1 uses an Aegilops speltoides dataset and results show that tested repeat sequences have B chromosome origin. Example_2 uses the winter barley specific gene VRN-H2 and results show that it is absent in spring barley cultivar Morex. Example_3 uses...

The e!DAL JAVA-API - Store, Share and Cite Primary Data in Life Sciences

Daniel Arend
Current strategies for primary data management towards effective data publication, retrieval, sharing and citation require enhanced platforms. One driving force is the recent developments in biotechnology. It is attended by a strong growth of scientific primary data. For example, “Next-Generation-Sequencing” or “Plant-Phenotyping” technologies produce a huge amount of primary data. Its analysis and publication is one pillar in modern life science research. Consequently, the responsible use and efficient availability of digital resources is an important...

Screening of wild potato genetic resources for resistance against late blight on tubers

Silvia Bachmann-Pfabe
This data set contains results of the Phytophthora infestans (Mont.) de Bary resistance screening of wild potato accessions during the years 1995 to 2016 maintained at the Gross Luesewitz Potato Collections (GLKS) of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK).

Raw image files from an investigation of vegetative biomass growth in well-watered and drought stress conditions in a Hordeum vulgare set (2011-05-27 to 2011-07-24)

Kerstin Neumann
This dataset contains 340149 raw image files of a high-throughput plant phenotyping experiment, which was run from 2011-05-27 to 2011-07-24. The vegetative biomass growth of a small set of Hordeum vulgare plants has been monitored. The files are described using the ISA-Tab format and fulfill the MIAPPE recommendations. The raw images were processed by the barley analysis pipelines of the IAP software (version 1.1.2; https://doi.org/10.1104/pp.113.233932). The analysed results were exported in the ‘1121KN_IAP_export.xlsx’ file.

Poster_DI_IPK-Evaluation_2012

Swetlana Friedel
Poster_DI_IPK-Evaluation_2012

Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes

Sebastian Beier
Software package for assembling paired-end BAC read data and scaffolding the generated paired-end assemblies with mate-pair read data.

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